Medication reconciliation is crucial to prevent medication errors. In Denmark, primary and secondary care physicians can prescribe medication in the same electronic prescribing system known as the Shared Medication Record (SMR). However, the SMR is not always updated by physicians, which can lead to discrepancies between the SMR and patients’ actual use of medication. These discrepancies may compromise patient safety upon admission to the emergency department (ED). Here, we investigated (a) the occurrence of discrepancies, (b) factors associated with discrepancies, and (c) the percentage of patients accessible to a clinical pharmacist during pharmacy working hours. The study included all patients age ≥ 18 years who were admitted to the Hvidovre Hospital ED on three consecutive days in June 2020. The clinical pharmacists performed medicines reconciliation to identify prescribing discrepancies. In total, 100 patients (52% male; median age 66.5 years) were included. The patients had a median of 10 [IQR 7–13] medications listed in the SMR and a median of two [IQR 1–3.25] discrepancies. Factors associated with increased rate of prescribing discrepancies were age < 65 years, time since last update of the SMR ≥ 115 days, and patients’ self-dispensing their medications. Eighty-four percent of patients were available for medicines reconciliations during the normal working hours of the clinical pharmacist. In conclusion, we found that discrepancies between the SMR and patients’ actual medication use upon admission to the ED are frequent, and we identified several risk factors associated with the increased rate of discrepancies.